7RN0

Crystal structure of the SARS-CoV-2 (COVID-19) main protease in complex with inhibitor Jun9-57-3R


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7KX5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29325 % 3350, 0.2 M AmSO4, 0.1 M HEPES 7.5
Crystal Properties
Matthews coefficientSolvent content
1.9737.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.42α = 90
b = 53.43β = 101.37
c = 112.031γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2021-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97890APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.255092.40.0710.0870.050.9947.62.711614
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.3295.40.7090.8650.4880.6432.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT7KX52.2548.051101159791.850.21510.21380.241RANDOM53.388
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-2.540.71-0.752.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.263
r_dihedral_angle_4_deg19.9
r_dihedral_angle_3_deg17.813
r_dihedral_angle_1_deg7.904
r_angle_refined_deg1.62
r_angle_other_deg1.312
r_chiral_restr0.065
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.263
r_dihedral_angle_4_deg19.9
r_dihedral_angle_3_deg17.813
r_dihedral_angle_1_deg7.904
r_angle_refined_deg1.62
r_angle_other_deg1.312
r_chiral_restr0.065
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2326
Nucleic Acid Atoms
Solvent Atoms22
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
MOLREPphasing